pepquery2: pepquery2.xml annotate

annotate pepquery2.xml @ 2:3b2874c58bcd draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071

author	galaxyp
date	Tue, 25 Oct 2022 16:06:20 +0000
parents	6b5ce9e2b0d0
children	d8962e547c9c

rev	line source
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	1 <tool id="pepquery2" name="PepQuery2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	3 <macros>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	4 <import>macros.xml</import>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	5 </macros>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	6 <requirements>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	8 </requirements>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	9 <stdio>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	10 <exit_code range="1:" level="fatal" description="Failed" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	11 <regex match="Exception"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	12 source="stderr"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	13 level="fatal"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	14 description="java Exception" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	15 </stdio>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	16 <command><![CDATA[
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	17 @CMD_IMPORTS@
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	18 #if $req_inputs.db_type.db_type_selector == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	19 #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_type.db_file.display_name.split('/')[-1])) + ".fa"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	20 ln -s '$req_inputs.db_type.db_file' '$db_file' &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	21 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	22 #if $req_inputs.ms_dataset.ms_dataset_type == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	23 @INDEX_SPECTRUM_FILES@
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	24 $index_spectrum_files($ms_index.files_path, $req_inputs.ms_dataset.spectrum_files) &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	25 #elif $req_inputs.ms_dataset.ms_dataset_type == 'indexed'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	26 #if $os.path.exists($os.path.join($req_inputs.ms_dataset.index.extra_files_path, 'summary.txt'))
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	27 #set $index_dir = 'index_dir'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	28 ln -s '$req_inputs.ms_dataset.index.extra_files_path' index_dir &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	29 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	30 #raise ValueError
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	31 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	32 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	33 ## PepQuery command
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	34 pepquery
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	35 -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	36 #if $validation.task_type == "known"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	37 -s 2 $validation.decoy
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	38 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	39 -s 1
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	40 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	41 #if $req_inputs.ms_dataset.ms_dataset_type in ['history', 'indexed']
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	42 -ms '$index_dir'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	43 #elif $req_inputs.ms_dataset.ms_dataset_type in ['PepQueryDB', 'public']
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	44 -b '$req_inputs.ms_dataset.dataset'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	45 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	46
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	47 #if $req_inputs.db_type.db_type_selector == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	48 -db '$db_file'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	49 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	50 -db '$req_inputs.db_type.db_id'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	51 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	52 #if $req_inputs.input_type.input_type_selector == 'peptide'
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	53 -t $req_inputs.input_type.input_type_selector
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	54 -i '$req_inputs.input_type.multiple.input'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	55 #else
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	56 -t $req_inputs.input_type.input_type_selector
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	57 #if $req_inputs.input_type.input_type_selector == 'protein'
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	58 #if $req_inputs.input_type.multiple.protein_input_selector == 'identifier'
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	59 #set $prot_id = str($req_inputs.input_type.multiple.input).replace('\|','\\|')
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	60 -i '"$prot_id"'
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	61 #else
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	62 -i '$req_inputs.input_type.multiple.input'
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	63 #end if
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	64 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	65 -i '$req_inputs.input_type.input'
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	66 #if $req_inputs.input_type.input_type_selector == 'DNA'
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	67 #if $req_inputs.input_type.frame == 'None'
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	68 -frame '0'
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	69 #else
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	70 -frame '$req_inputs.input_type.frame'
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	71 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	72 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	73 -anno '$req_inputs.input_type.anno'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	74 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	75 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	76 #end if
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	77 #if $req_inputs.indexType
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	78 -indexType $req_inputs.indexType
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	79 #end if
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	80
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	81 #if $modifications.fixed_mod
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	82 -fixMod '$modifications.fixed_mod'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	83 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	84 #if $modifications.var_mod
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	85 -varMod '$modifications.var_mod'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	86 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	87 #if $digestion.enzyme
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	88 -e '$digestion.enzyme'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	89 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	90 #if $digestion.max_missed_cleavages
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	91 -c '$digestion.max_missed_cleavages'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	92 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	93
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	94 #if $modifications.max_mods
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	95 -maxVar '$modifications.max_mods'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	96 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	97 $modifications.unmodified
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	98 $modifications.aa
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	99 #if $ms_params.tolerance_params.precursor_tolerance
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	100 -tol '$ms_params.tolerance_params.precursor_tolerance'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	101 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	102
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	103 #if $ms_params.tolerance_params.precursor_unit
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	104 -tolu '$ms_params.tolerance_params.precursor_unit'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	105 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	106 #if $ms_params.tolerance_params.tolerance
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	107 -itol '$ms_params.tolerance_params.tolerance'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	108 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	109 #if $ms_params.search.frag_method
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	110 -fragmentMethod '$ms_params.search.frag_method'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	111 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	112 #if $ms_params.search.scoring_method
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	113 -m '$ms_params.search.scoring_method'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	114 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	115 $ms_params.search.extra_score_validation
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	116 #if $ms_params.search.max_charge
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	117 -maxCharge '$ms_params.search.max_charge'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	118 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	119 #if $ms_params.search.min_charge
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	120 -minCharge '$ms_params.search.min_charge'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	121 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	122 #if $ms_params.search.min_peaks
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	123 -minPeaks '$ms_params.search.min_peaks'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	124 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	125 #if $ms_params.search.isotope_error
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	126 -ti '$ms_params.search.isotope_error'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	127 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	128 #if $ms_params.search.min_score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	129 -minScore '$ms_params.search.min_score'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	130 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	131 #if $ms_params.search.min_length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	132 -minLength '$ms_params.search.min_length'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	133 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	134 #if $ms_params.search.max_length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	135 -maxLength '$ms_params.search.max_length'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	136 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	137 #if $ms_params.search.num_random_peptides
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	138 -n '$ms_params.search.num_random_peptides'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	139 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	140 #if 'psm_annotation.txt' in $outputs_selected
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	141 -plot
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	142 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	143 $fast
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	144 -o pepquery_output
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	145 \| tee >(sed "s/\x1b[^m]*m//g" > log.txt)
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	146 #set $flist = str($outputs_selected).replace(',',' ').replace('ms_index','')
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	147 && for i in $flist; do for f in `find pepquery_output// -name \$i`; do cat \$f >> pepquery_output/\${i}; done; done
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	148 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	149 ]]>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	150 </command>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	151 <inputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	152 <conditional name="validation">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	153 <param name="task_type" argument="-s" type="select" label="Validation Task Type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	154 <option value="novel" selected="true">novel peptide/protein validation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	155 <option value="known">known peptide/protein validation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	156 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	157 <when value="novel"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	158 <when value="known">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	159 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	160 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	161 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	162 <section name="req_inputs" title="Input Data" expanded="true">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	163 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	164 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	165 <option value="peptide">peptide</option>
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	166 <option value="protein">protein</option>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	167 <option value="DNA">DNA (translate to protein sequences)</option>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	168 <!-- these are not working with pepquery version 1.6
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	169 <option value="3">VCF (translate to protein sequences)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	170 <option value="4">BED (translate to protein sequences)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	171 <option value="5">GTF (translate to protein sequences)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	172 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	173 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	174 <when value="peptide">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	175 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	176 <param name="peptide_input_selector" type="select" label="Peptides?">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	177 <option value="multiple">Peptide list from your history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	178 <option value="single">Single peptide entered as text</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	179 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	180 <when value="multiple">
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	181 <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	182 <help>Peptide sequence file containing peptides which you want to search (no column headers).
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	183 First column is am peptide sequence. Optional second column is spectrum title.
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	184 </help>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	185 </param>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	186 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	187 <when value="single">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	188 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	189 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	190 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	191 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	192 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	193 </when>
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	194 <when value="protein">
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	195 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	196 <param name="protein_input_selector" type="select" label="Proteins?">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	197 <option value="multiple">Protein fasta from your history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	198 <option value="single">Single protein entered as text</option>
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	199 <option value="identifier">Protein Identifier from selected Protein Reference Database</option>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	200 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	201 <when value="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	202 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	203 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	204 <when value="single">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	205 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	206 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	207 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	208 </when>
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	209 <when value="identifier">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	210 <param name="input" argument="-i" type="text" label="Protein Identifier" help="Protein ID from the selected Protein Reference Database. E.g. sp\|P07205\|PGK2_HUMAN from swissprot:human">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	211 <sanitizer invalid_char="">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	212 <valid initial="string.ascii_letters,string.digits">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	213 <add value="\|" />
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	214 </valid>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	215 </sanitizer>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	216 <validator type="regex" message="Spaces not allowed in ID">^[^ ]+$</validator>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	217 </param>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	218 </when>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	219 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	220 </when>
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	221 <when value="DNA">
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	222 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	223 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	224 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	225 <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	226 <option value="1">1</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	227 <option value="2">2</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	228 <option value="3">3</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	229 <option value="4">4</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	230 <option value="5">5</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	231 <option value="6">6</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	232 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	233 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	234 <!-- these are not working with pepquery version 1.6
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	235 <when value="3">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	236 <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	237 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	238 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	239 <when value="4">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	240 <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	241 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	242 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	243 <when value="5">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	244 <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	245 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	246 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	247 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	248 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	249 <conditional name="db_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	250 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	251 <option value="history">history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	252 <option value="download">download</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	253 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	254 <when value="history">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	255 <param name="db_file" argument="-db" type="data" format="fasta" label="Protein Reference Database File" help="an input sequence that matches a reference will be ignored." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	256 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	257 <when value="download">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	258 <param name="db_id" type="text" value="" label="Public protein sequence database">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	259 <help>Currently supported dowloads: gencode:human, swissprot:human, refseq:human</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	260 <option value="gencode:human">gencode:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	261 <option value="swissprot:human">swissprot:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	262 <option value="refseq:human">refseq:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	263 <validator type="regex" message="">^(swissprot\|refseq\|gencode):(human)$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	264 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	265 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	266 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	267 <conditional name="ms_dataset">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	268 <param name="ms_dataset_type" type="select" label="MS/MS dataset to search" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	269 <option value="history"> Spectrum Datasets from history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	270 <option value="indexed">Indexed MS/MS spectrums</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	271 <option value="PepQueryDB">PepQueryDB</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	272 <option value="public">public proteomics data repositories</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	273 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	274 <when value="history">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	275 <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	276 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	277 <when value="indexed">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	278 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	279 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	280 <when value="PepQueryDB">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	281 <param name="dataset" argument="-b" type="text" value="" label="PepQueryDB dataset">
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	282 <help>PepQueryDB dataset IDs (separated by commas).</help>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	283 <expand macro="pepquerydb_options" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	284 <validator type="regex" message="PepQueryDB dataset_name(,dataset_name)">^[a-zA-Z][^,](,[a-zA-Z][^,])*$</validator>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	285 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	286 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	287 <when value="public">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	288 <param name="dataset" type="text" value="" label="Public dataset">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	289 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD\|MSV\|JPST).*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	290 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	291 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	292 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	293
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	294 <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	295 <option value="1">index (1-based) in MGF</option>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	296 <option value="2">spectrum title in MGF</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	297 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	298 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	299
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	300 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	301 <help>Currently supported set names start with: MS1 or TMT</help>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	302 <option value="MS1_H_MS2_H_LF">MS1_H_MS2_H_LF</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	303 <option value="MS1_H_MS2_L_LF">MS1_H_MS2_L_LF</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	304 <option value="TMT10_11">TMT10_11</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	305 <option value="TMT10_11_MS2_L">TMT10_11_MS2_L</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	306 <option value="TMT10_11_MS2_L_phosphorylation">TMT10_11_MS2_L_phosphorylation</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	307 <option value="TMT10_11_acetylation">TMT10_11_acetylation</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	308 <option value="TMT10_11_glycosylation">TMT10_11_glycosylation</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	309 <option value="TMT10_11_phosphorylation">TMT10_11_phosphorylation</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	310 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	311 </param>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	312
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	313 <section name="modifications" title="Modifications" expanded="false">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	314 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	315 <help>Default: 1: Carbamidomethylation of C [57.02146372057]</help>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	316 <expand macro="modifications" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	317 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	318 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	319 <help>Default: 2: Oxidation of M [15.99491461956]</help>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	320 <expand macro="modifications" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	321 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	322
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	323 <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications Default: 3" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	324 <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	325 <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	326 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	327
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	328 <section name="digestion" title="Digestion" expanded="false">
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	329 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion. Default: Trypsin" >
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	330 <option value="0">Non enzyme</option>
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	331 <option value="1">Trypsin</option>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	332 <option value="2">Trypsin (no P rule)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	333 <option value="3">Arg-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	334 <option value="4">Arg-C (no P rule)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	335 <option value="5">Arg-N</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	336 <option value="6">Glu-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	337 <option value="7">Lys-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	338 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	339 <param name="max_missed_cleavages" argument="-c" type="integer" value="" optional="true" label="Max Missed Cleavages" help="The max missed cleavages" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	340 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	341
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	342 <section name="ms_params" title="Mass spectrometer" expanded="false">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	343 <section name="tolerance_params" title="Tolerance" expanded="true">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	344 <param name="precursor_tolerance" argument="-tol" type="integer" value="" optional="true" label="Precursor Tolerance" help="The error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data. Default: 10" />
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	345 <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance. Default: ppm">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	346 <option value="ppm">ppm</option>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	347 <option value="Da">Da</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	348 </param>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	349 <param name="tolerance" argument="-itol" type="float" value="" optional="true" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit. Default: 0.6 Da" />
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	350 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	351
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	352 <section name="search" title="PSM" expanded="false">
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	353 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method" help="Default: CID/HCD">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	354 <option value="1">CID/HCD</option>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	355 <option value="2">ETD</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	356 </param>
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	357 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method" help="Default: HyperScore">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	358 <option value="1">HyperScore</option>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	359 <option value="2">MVH</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	360 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	361 <param name="extra_score_validation" argument="-x" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Add extra score validation" help="use two scoring algorithms for peptide identification" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	362 <param name="min_charge" argument="-minCharge" type="integer" value="" optional="true" label="Minimum Charge" help="The minimum charge to consider if the charge state is not available. Default: 2"/>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	363 <param name="max_charge" argument="-maxCharge" type="integer" value="" optional="true" label="Maximum Charge" help="The maximum charge to consider if the charge state is not available. Default: 3" />
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	364 <param name="min_peaks" argument="-minPeaks" type="integer" value="" optional="true" label="Minimum Peaks" help="Min peaks in spectrum. Default: 10" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	365 <param name="isotope_error" argument="-ti" type="text" value="" optional="true" label="Isotope peak error range">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	366 <help>A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	367 <validator type="regex" message="">^((-2,)?-1,)?0(,1(,2)?)?$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	368 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	369 <param name="min_score" argument="-minScore" type="integer" value="" min="0" optional="true" label="Minimum Score" help="Minimum score to consider for peptide searching. Default: 12" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	370 <param name="min_length" argument="-minLength" type="integer" value="" min="0" optional="true" label="Minimum length of peptide" help="The maximum length of peptide to consider. Default: 7" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	371 <param name="max_length" argument="-maxLength" type="integer" value="" min="0" optional="true" label="Maximum length of peptide" help="The maximum length of peptide to consider. Default: 45" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	372 <param name="num_random_peptides" argument="-n" type="integer" value="" min="0" optional="true" label="Number of Random Peptides" help="The number of random peptides. Default: 1000" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	373 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	374 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	375
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	376 <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	377 <option value="psm.txt" selected="true">psm.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	378 <option value="psm_rank.txt" selected="true">psm_rank.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	379 <option value="psm_rank.mgf" selected="true">psm_rank.mgf</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	380 <option value="psm_annotation.txt" selected="true">psm_annotation.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	381 <option value="psm_type.txt" selected="false">psm_type.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	382 <option value="detail.txt" selected="true">detail.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	383 <option value="ptm.txt" selected="true">ptm.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	384 <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	385 <option value="ms_index" selected="true">MS/MS Index</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	386 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	387 <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	388 </inputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	389 <outputs>
2 3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	390 <data name="log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071 galaxyp parents: 1 diff changeset	391 </data>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	392 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	393 </data>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	394 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	395 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	396 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	397 <data name="psm_txt" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: psm.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	398 <filter>'psm.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	399 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	400 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	401 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	402 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	403 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	404
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	405 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: psm_rank.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	406 <filter>'psm_rank.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	407 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	408 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	409 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm,confident,ref_delta_score,mod_delta_score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	410 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	411 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	412
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	413 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: psm_rank.mgf">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	414 <filter>'psm_rank.mgf' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	415 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	416 <data name="psm_type_txt" format="tabular" from_work_dir="pepquery_output/psmi_type.txt" label="${tool.name} on ${on_string}: psm_type.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	417 <filter>'psm_type.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	418 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	419 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	420 <action name="column_names" type="metadata" default="peptide,spectrum_title,type" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	421 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	422 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	423 <data name="psm_annotation_txt" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: psm_annotation.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	424 <filter>'psm_annotation.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	425 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	426 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	427 <action name="column_names" type="metadata" default="peptide,modification,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	428 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	429 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	430 <data name="detail_txt" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: detail.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	431 <filter>'detail.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	432 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	433 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	434 <action name="column_names" type="metadata" default="spectrum_title,peptide,modification,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	435 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	436 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	437
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	438 <data name="ptm_txt" format="tabular" from_work_dir="pepquery_output/ptm.txt" label="${tool.name} on ${on_string}: ptm.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	439 <filter>'ptm.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	440 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	441 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	442 <action name="column_names" type="metadata" default="spectrum_title,peptide,charge,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,modification,score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	443 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	444 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	445 <data name="ptm_detail_txt" format="tabular" from_work_dir="pepquery_output/ptm_detail.txt" label="${tool.name} on ${on_string}: ptm_detail.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	446 <filter>'ptm_detail.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	447 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	448 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	449 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,ptm_spectrum_title,ptm_peptide,ptm_charge,ptm_exp_mass,ptm_pep_mass,ptm_tol_ppm,ptm_tol_da,ptm_isotope_error,ptm_modification,ptm_score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	450 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	451 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	452
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	453 </outputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	454 <tests>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	455 <!-- Test-1 PepQueryDB peptide gencode:human -->
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	456 <test>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	457 <conditional name="validation">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	458 <param name="task_type" value="novel"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	459 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	460 <section name="req_inputs">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	461 <conditional name="input_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	462 <param name="input_type_selector" value="peptide"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	463 <conditional name="multiple">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	464 <param name="peptide_input_selector" value="single" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	465 <param name="input" value="LVVVGADGVGK"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	466 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	467 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	468 <conditional name="db_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	469 <param name="db_type_selector" value="download" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	470 <param name="db_id" value="gencode:human"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	471 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	472 <conditional name="ms_dataset">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	473 <param name="ms_dataset_type" value="PepQueryDB"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	474 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	475 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	476 <param name="indexType" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	477 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	478 <param name="parameter_set" value=""/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	479 <section name="modifications">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	480 <param name="fixed_mod" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	481 <param name="var_mod" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	482 <param name="max_mods" value="3"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	483 <param name="unmodified" value="True"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	484 <param name="aa" value="False"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	485 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	486 <section name="digestion">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	487 <param name="enzyme" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	488 <param name="max_missed_cleavages" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	489 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	490 <section name="ms_params">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	491 <section name="tolerance_params">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	492 <param name="precursor_tolerance" value="10"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	493 <param name="precursor_unit" value="ppm"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	494 <param name="tolerance" value="0.6"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	495 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	496 <section name="search">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	497 <param name="frag_method" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	498 <param name="scoring_method" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	499 <param name="extra_score_validation" value="False"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	500 <param name="min_charge" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	501 <param name="max_charge" value="3"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	502 <param name="min_peaks" value="10"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	503 <param name="isotope_error" value="0"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	504 <param name="min_score" value="12"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	505 <param name="min_length" value="7"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	506 <param name="max_length" value="45"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	507 <param name="num_random_peptides" value="1000"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	508 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	509 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	510 <output name="psm_txt">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	511 <assert_contents>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	512 <has_text text="LVVVGADGVGK" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	513 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	514 </assert_contents>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	515 </output>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	516 </test>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	517
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	518 <!-- Test-2 MGF peptide Uniprot.fasta -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	519 <test>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	520 <conditional name="validation">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	521 <param name="task_type" value="novel"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	522 </conditional>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	523 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	524 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	525 <param name="input_type_selector" value="peptide"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	526 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	527 <param name="peptide_input_selector" value="single" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	528 <param name="input" value="ELGSSDLTAR"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	529 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	530 </conditional>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	531 <conditional name="db_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	532 <param name="db_type_selector" value="history" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	533 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	534 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	535 <conditional name="ms_dataset">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	536 <param name="ms_dataset_type" value="history"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	537 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	538 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	539 <param name="indexType" value="1"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	540 </section>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	541 <param name="parameter_set" value=""/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	542 <section name="modifications">
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	543 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	544 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	545 <param name="fixed_mod" value="1,21,22"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	546 <!-- 2: Oxidation of M [15.99491461956] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	547 <param name="var_mod" value="2"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	548 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	549 <param name="unmodified" value="True"/>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	550 <param name="aa" value="False"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	551 </section>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	552 <section name="digestion">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	553 <param name="enzyme" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	554 <param name="max_missed_cleavages" value="2"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	555 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	556 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	557 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	558 <param name="precursor_tolerance" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	559 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	560 <param name="tolerance" value="0.6"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	561 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	562 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	563 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	564 <param name="scoring_method" value="1"/>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	565 <param name="extra_score_validation" value="False"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	566 <param name="min_charge" value="2"/>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	567 <param name="max_charge" value="3"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	568 <param name="min_peaks" value="10"/>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	569 <param name="isotope_error" value="0"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	570 <param name="min_score" value="12"/>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	571 <param name="min_length" value="7"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	572 <param name="max_length" value="45"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	573 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	574 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	575 </section>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	576 <output name="psm_txt">
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	577 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	578 <has_text text="ELGSSDLTAR" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	579 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	580 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	581 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	582 <assert_contents>
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	583 <has_text text="ELGSSDLTAR" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	584 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/>
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	585 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	586 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	587 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	588
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	589 </tests>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	590 <help><![CDATA[
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	591 PepQuery2
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	592
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	593 PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	594
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	595
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	596 PepQuery_ is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	597
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	598 PepQuery2 leverages a new MS/MS indexing approach and cloud storage to enable ultrafast, targeted identification of both novel and known peptides. PepQuery2 allows users to search more than one billion MS/MS data indexed in the PepQueryDB from any computers with internet access. It also supports direct analysis of user provided MS/MS data, any public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	599
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	600 Inputs
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	601 - A sequence to match, one of the following:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	602
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	603 - A peptide string (or strings separated by commas)
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	604 - A history dataset with a list of peptides
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	605 - A protein string or a history dataset with a protein fasta
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	606 - A DNA string that is at least 60 base pairs in length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	607
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	608
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	609 - MS/MS data used for identification, one of the following:
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	610
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	611 - Mass Spectrometry history datasets in MGF, mzML, or mzXML format
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	612 - An Indexed MS/MS dataset (from previous PepQuery2 run or from PepQuery2 index tool.)
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	613 - PepQueryDB dataset IDs
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	614
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	615 ..
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	616
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	617 Multiple datasets from PepQueryDB must be separated by comma. A pattern to match datasets in PepQueryDB is also supported, for example, use 'CPTAC' to search all datasets contain 'CPTAC'. In addition, dataset selection from PepQueryDB based on data type (w:global proteome, p:phosphorylation, a:acetylation, u:ubiquitination, g:glycosylation) is also supported. For example, use 'p' to search all phosphoproteomics datasets in PepQueryDB. The PepQuery2 Show Sets tool will list available PepQueryDB datasets.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	618
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	619
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	620 - Dataset IDs from public proteomics data repositories: PRIDE, MassIVE, jPOSTrepo and iProX
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	621
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	622 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	623
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	624 Dataset ID from public proteomics data repositories, one dataset is supported for each analysis. For example, use 'PXD000529' to use all MS/MS data from dataset PXD000529 or use 'PXD000529:LM3' to use data files containing LM3 from dataset PXD000529
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	625
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	626 - A reference protein fasta database, novel peptides matching a reference sequence will be excluded.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	627
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	628 - A protein fasta file
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	629 - The ID for a public reference protein database from RefSeq, GENCODE, Ensembl or UniProt.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	630
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	631
1 6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	632 Options
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	633
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	634 - MS/MS searching parameter set name
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	635
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	636 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	637
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	638 Setting a parameter set name will change defaults for various options, These may be overridden by manually setting the option.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	639 The PepQuery2 Show Sets tool PepQuery Predefined Parameter Sets will list those available along with the option values that will be set.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	640 The PepQuery2 Show Sets tool PepQuery Datasets column parameter_set column for each PepQueryDB dataset.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	641
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	642
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	643 - Override default options
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	644
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	645 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	646
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	647 Values for modifications are provided in a select list.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	648 The PepQuery2 Show Sets tool PepQuery Modifications lists all available modifications.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457 galaxyp parents: 0 diff changeset	649
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	650 Outputs
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	651 - Parameters:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	652
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	653 - parameters used in the search
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	654
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	655 - PSM - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	656
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	657 - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	658
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	659 - PSM Rank - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	660
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	661 - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank n_ptm
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	662
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	663 - An MGF with the best matching spectrums
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	664
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	665 - Detail - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	666
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	667 - spectrum_title peptide modification pep_mass score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	668
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	669 - PSM annotation - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	670
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	671 - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	672
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	673 - PTM - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	674
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	675 - spectrum_title peptide charge exp_mass pep_mass tol_ppm tol_da isotope_error modification score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	676
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	677 - PTM Detail - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	678
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	679 - peptide modification n spectrum_title charge exp_mass tol_ppm tol_da isotope_error pep_mass mz score n_db total_db n_random total_random pvalue rank ptm_spectrum_title ptm_peptide ptm_charge ptm_exp_mass ptm_pep_mass ptm_tol_ppm ptm_tol_da ptm_isotope_error ptm_modification ptm_score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	680
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	681 - An Indexed MS/MS dataset when MS/MS data is MGF, mzML, or mzXML history datasets
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	682
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	683 The n_ptm field is added when using unrestricted modification searching (-um).
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	684
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	685 .. _PepQuery: http://pepquery.org/document.html
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	686
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	687 ]]></help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	688 <expand macro="citations" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	689 </tool>

Mercurial > repos > galaxyp > pepquery2

annotate pepquery2.xml @ 2:3b2874c58bcd draft